Gutenberg Open Science

The Open Science Repository of Johannes Gutenberg University Mainz.

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Recent Submissions

  • Item type: Item , ZeitschriftenaufsatzAccess status: Open Access ,
    RMapAlign3N : fast mapping of 3N-Reads
    (2025) Müller, Andre; Wichmann, Alexander; Kallenborn, Felix; Hildebrandt, Andreas; Schmidt, Bertil
    Nucleotide conversion sequencing techniques are frequently used for the detection of various types of chemical modifications at nucleotide level. However, mapping of chemically treated reads to large reference sequences that contain only three nucleotides can be highly compute-intensive. We present RMapAlign3N—an efficient yet accurate tool for mapping of 3 N-reads to reference genomes or transcriptomes that leverages the power of modern multi-core CPUs. Our performance evaluation using real and simulated data shows that RMapAlign3N is faster and more scalable than prior CPU-based approaches including HISAT-3N, BSMAP, Bismark, and SLAM-DUNK for BS-seq and SLAM-seq data at competitive accuracy.
  • Item type: Item , ZeitschriftenaufsatzAccess status: Open Access ,
    Assessing the exercise-related kinetics of circulating cell-free DNA, circulating tumour DNA, DNase I activity and cytokines in patients with solid tumours : a pilot study
    (2025) Neuberger, Elmo W. I.; Brahmer, Alexandra; Ehlert, Tobias; Botzenhardt, Suzan; De Falco, Alfonso; Enders, Birgit; Hähnel, Patricia S.; Heintz, Achim; Schimanski, Carl C.; Kindler, Thomas; Simon, Perikles
    Circulating cell-free DNA (cfDNA), circulating tumour DNA (ctDNA) and inflammatory cytokines have prognostic and predictive value in oncology. However, the effects of acute exercise on cfDNA levels are unknown. Here, we explore the kinetics of cfDNA, ctDNA and cytokines upon an incremental exercise test in a pilot cohort of cancer patients compared with healthy control subjects. Patients with solid tumours (n = 12) and age-matched control subjects (n = 6) were recruited to perform an all-out cardiopulmonary bicycle test. Blood samples were collected before (Pre), directly after (Post) and 90 min after the test (+90 min), and the cfDNA, ctDNA (Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations), DNase I activity and cytokine levels were measured. Cardiopulmonary exercise testing was easily feasible in cancer patients, and data from eight patients and five control subjects were available for exploratory statistical evaluation. The cfDNA levels increased from Pre to Post and decreased to baseline at +90 min in all subjects. The cfDNA concentrations and DNase I activity were clearly correlated in the control but not in the cancer group. Neutrophil-associated myeloperoxidase (MPO), calprotectin (MRP 8/14), and lipocalin A (NGAL) showed strong responses to exercise. The percentage of ctDNA, detected in only one cancer patient, decreased after acute exercise. In our study, we could safely perform cardiopulmonary exercise testing with patients with different cancer entities and subsequently run biomarker analyses. Our results hint at an exercise-triggered release of cfDNA and neutrophil-derived cytokines in cancer patients.
  • Item type: Item , ZeitschriftenaufsatzAccess status: Open Access ,
    Psychosocial work stress, resilience and the risk of tinnitus : results from a population-based cohort study
    (2025) Hackenberg, Berit; Döge, Julia; O’Brien, Karoline; Nübling, Matthias; Dietz, Pavel; Beutel, Manfred E.; Reinwarth, Anna Celine; Lackner, Karl J.; Tüscher, Oliver; Schattenberg, Jörn M.; Hobohm, Lukas; Münzel, Thomas; Wild, Philipp S.; Schuster, Alexander K.; Schmidtmann, Irene; Chalabi, Julian; Matthias, Christoph; Bahr-Hamm, Katharina
    Background and Objectives: Tinnitus is a common symptom in otolaryngologic practice. Although its pathophysiology is multifactorial and remains mostly unclear, it can be correlated to stress and psychological comorbidities. The aim of this study was to assess the correlation between the occurrence of tinnitus and psychosocial work stress (measured using the German COPSOQ-III, a validated instrument) in a large working population. Materials and Methods: The Gutenberg Health Study is a single-center, prospective, observational cohort study. Participants of working age were included and surveyed using the German COPSOQ-III; they were interviewed regarding the occurrence of tinnitus (yes/no) and stratified according to their resilience (measured using the Brief Resilient Coping Scale). Results: A total of 4933 participants of working age were included in the study cohort, in which tinnitus was reported with a prevalence of 26.3%. Participants with tinnitus answered more negatively in all COPSOQ scales, although not all differences were statistically significant. The scales Emotional Demands, Work Privacy Conflicts, Work Environment/Physical Demands and Insecurity over Working Conditions showed especially high differences in means. In addition, all effect scales showed significant differences between participants with and without tinnitus. The prevalence of tinnitus decreased with increasing resilience. Conclusions: Tinnitus is a symptom highly correlated with psychosocial work stress. As such, it represents a significant health burden within the working community.